WW domain

The WW domain^[2] (also known as the rsp5-domain^[3] or WWP repeating motif^[4]) is a modular protein domain that mediates specific interactions with protein ligands. This domain is found in a number of unrelated signaling and structural proteins and may be repeated up to four times in some proteins.^[2][3][4][5] Apart from binding preferentially to proteins that are proline-rich, with particular proline-motifs, [AP]-P-P-[AP]-Y, some WW domains bind to phosphoserine- and phosphothreonine-containing motifs.^[6]

WW domain
Structure of the human mitotic rotamase Pin1.[1]
Identifiers
Symbol	WW
Pfam	PF00397
InterPro	IPR001202
PROSITE	PDOC50020
SCOP2	1pin / SCOPe / SUPFAM
CDD	cd00201
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

Structure and ligands

The WW domain is one of the smallest protein modules, composed of only 40 amino acids, which mediates specific protein-protein interactions with short proline-rich or proline-containing motifs.^[6] Named after the presence of two conserved tryptophans (W), which are spaced 20-22 amino acids apart within the sequence,^[2] the WW domain folds into a meandering triple-stranded beta sheet.^[7] The identification of the WW domain was facilitated by the analysis of two splice isoforms of YAP gene product, named YAP1-1 and YAP1-2, which differed by the presence of an extra 38 amino acids. These extra amino acids are encoded by a spliced-in exon and represent the second WW domain in YAP1-2 isoform.^[2][8]

The first structure of the WW domain was determined in solution by NMR approach.^[7] It represented the WW domain of human YAP in complex with peptide ligand containing Proline-Proline-x–Tyrosine (PPxY where x = any amino acid) consensus motif.^[6][7] Recently, the YAP WW domain structure in complex with SMAD-derived, PPxY motif-containing peptide was further refined.^[9] Apart from the PPxY motif, certain WW domains recognize LPxY motif (where L is Leucine),^[10] and several WW domains bind to phospho-Serine-Proline (p-SP) or phospho-Threonine-Proline (p-TP) motifs in a phospho-dependent manner.^[11] Structures of these WW domain complexes confirmed molecular details of phosphorylation-regulated interactions.^[1][12] There are also WW domains that interact with polyprolines that are flanked by arginine residues or interrupted by leucine residues, but they do not contain aromatic amino acids.^[13][14]

Signaling function

The WW domain is known to mediate regulatory protein complexes in various signaling networks, including the Hippo signaling pathway.^[15] The importance of WW domain-mediated complexes in signaling was underscored by the characterization of genetic syndromes that are caused by loss-of-function point mutations in the WW domain or its cognate ligand. These syndromes are Golabi-Ito-Hall syndrome of intellectual disability caused by missense mutation in a WW domain^[16][17] and Liddle syndrome of hypertension caused by point mutations within PPxY motif.^[18][19]

Examples

A large variety of proteins containing the WW domain are known. These include; dystrophin, a multidomain cytoskeletal protein; utrophin, a dystrophin-like protein; vertebrate YAP protein, substrate of LATS1 and LATS2 serine-threonine kinases of the Hippo tumor suppressor pathway; Mus musculus (Mouse) NEDD4, involved in the embryonic development and differentiation of the central nervous system; Saccharomyces cerevisiae (Baker's yeast) RSP5, similar to NEDD4 in its molecular organization; Rattus norvegicus (Rat) FE65, a transcription-factor activator expressed preferentially in brain; Nicotiana tabacum (Common tobacco) DB10 protein, amongst others.^[20]

In 2004, the first comprehensive protein-peptide interaction map for a human modular domain was reported using individually expressed WW domains and genome predicted, PPxY-containing synthetic peptides.^[21] At present in the human proteome, 98 WW domains^[22] and more than 2000 PPxY-containing peptides,^[17] have been identified from sequence analysis of the genome.

Inhibitor

YAP is a WW domain-containing protein that functions as a potent oncogene.^[2][23] Its WW domains must be intact for YAP to act as a transcriptional co-activator that induces expression of proliferative genes.^[24] Recent study has shown that endohedral metallofullerenol, a compound that was originally developed as a contrasting agent for MRI (magnetic resonance imaging), has antineoplastic properties.^[25] Via molecular dynamic simulations, the ability of this compound to outcompete proline-rich peptides and bind effectively to the WW domain of YAP was documented.^[26] Endohedral metallofullerenol may represent a lead compound for the development of therapies for cancer patients who harbor amplified or overexpressed YAP.^[26][27]

In the study of protein folding

Because of its small size and well-defined structure, the WW domain was developed by the Gruebele and Kelly groups into a favorite subject of protein folding studies.^{[28][29][30][31][32][33]} Among these studies, the work of Rama Ranganathan^[34][35] and David E. Shaw are also notable.^[36][37] Ranganathan’s team has shown that a simple statistical energy function, which identifies co-evolution between amino acid residues within the WW domain, is necessary and sufficient to specify sequence that folds into native structure.^[35] Using such an algorithm, he and his team synthesized libraries of artificial WW domains that functioned in a very similar manner to their natural counterparts, recognizing class-specific proline-rich ligand peptides,^[34] The Shaw laboratory developed a specialized machine that allowed elucidation of the atomic level behavior of the WW domain on a biologically relevant time scale.^[36] He and his team employed equilibrium simulations of a WW domain and identified seven unfolding and eight folding events.^[37]

Being relatively short, 30 to 35 amino acids long, WW domain is amenable to chemical synthesis. It is cooperatively folded and can host chemically introduced non-canonical amino acids. Based on these properties, WW domain has been shown to be a versatile platform for the chemical interrogation of intramolecular interactions and conformational propensities in folded proteins.^[38]